Job ID = 6368674 SRX = SRX5402701 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:27:49 prefetch.2.10.7: 1) Downloading 'SRR8602935'... 2020-06-16T00:27:49 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:30:53 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:30:53 prefetch.2.10.7: 1) 'SRR8602935' was downloaded successfully Read 25786876 spots for SRR8602935/SRR8602935.sra Written 25786876 spots for SRR8602935/SRR8602935.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:04:48 25786876 reads; of these: 25786876 (100.00%) were unpaired; of these: 7394893 (28.68%) aligned 0 times 13558001 (52.58%) aligned exactly 1 time 4833982 (18.75%) aligned >1 times 71.32% overall alignment rate Time searching: 00:04:48 Overall time: 00:04:48 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 5613198 / 18391983 = 0.3052 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 16 Jun 2020 09:40:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402701/SRX5402701.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402701/SRX5402701.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402701/SRX5402701.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402701/SRX5402701.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 16 Jun 2020 09:40:59: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:40:59: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:41:05: 1000000 INFO @ Tue, 16 Jun 2020 09:41:10: 2000000 INFO @ Tue, 16 Jun 2020 09:41:16: 3000000 INFO @ Tue, 16 Jun 2020 09:41:22: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 16 Jun 2020 09:41:28: 5000000 INFO @ Tue, 16 Jun 2020 09:41:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402701/SRX5402701.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402701/SRX5402701.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402701/SRX5402701.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402701/SRX5402701.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 16 Jun 2020 09:41:29: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:41:29: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:41:34: 6000000 INFO @ Tue, 16 Jun 2020 09:41:35: 1000000 INFO @ Tue, 16 Jun 2020 09:41:40: 7000000 INFO @ Tue, 16 Jun 2020 09:41:41: 2000000 INFO @ Tue, 16 Jun 2020 09:41:46: 8000000 INFO @ Tue, 16 Jun 2020 09:41:48: 3000000 INFO @ Tue, 16 Jun 2020 09:41:52: 9000000 INFO @ Tue, 16 Jun 2020 09:41:54: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 16 Jun 2020 09:41:58: 10000000 INFO @ Tue, 16 Jun 2020 09:41:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402701/SRX5402701.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402701/SRX5402701.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402701/SRX5402701.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402701/SRX5402701.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 16 Jun 2020 09:41:59: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:41:59: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:42:00: 5000000 INFO @ Tue, 16 Jun 2020 09:42:04: 11000000 INFO @ Tue, 16 Jun 2020 09:42:05: 1000000 INFO @ Tue, 16 Jun 2020 09:42:07: 6000000 INFO @ Tue, 16 Jun 2020 09:42:10: 12000000 INFO @ Tue, 16 Jun 2020 09:42:12: 2000000 INFO @ Tue, 16 Jun 2020 09:42:13: 7000000 INFO @ Tue, 16 Jun 2020 09:42:15: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:42:15: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:42:15: #1 total tags in treatment: 12778785 INFO @ Tue, 16 Jun 2020 09:42:15: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:42:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:42:15: #1 tags after filtering in treatment: 12778785 INFO @ Tue, 16 Jun 2020 09:42:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:42:15: #1 finished! INFO @ Tue, 16 Jun 2020 09:42:15: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:42:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:42:16: #2 number of paired peaks: 518 WARNING @ Tue, 16 Jun 2020 09:42:16: Fewer paired peaks (518) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 518 pairs to build model! INFO @ Tue, 16 Jun 2020 09:42:16: start model_add_line... INFO @ Tue, 16 Jun 2020 09:42:16: start X-correlation... INFO @ Tue, 16 Jun 2020 09:42:16: end of X-cor INFO @ Tue, 16 Jun 2020 09:42:16: #2 finished! INFO @ Tue, 16 Jun 2020 09:42:16: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:42:16: #2 alternative fragment length(s) may be 1,17,33,548,598 bps INFO @ Tue, 16 Jun 2020 09:42:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402701/SRX5402701.05_model.r WARNING @ Tue, 16 Jun 2020 09:42:16: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:42:16: #2 You may need to consider one of the other alternative d(s): 1,17,33,548,598 WARNING @ Tue, 16 Jun 2020 09:42:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:42:16: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:42:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:42:18: 3000000 INFO @ Tue, 16 Jun 2020 09:42:19: 8000000 INFO @ Tue, 16 Jun 2020 09:42:24: 4000000 INFO @ Tue, 16 Jun 2020 09:42:26: 9000000 INFO @ Tue, 16 Jun 2020 09:42:31: 5000000 INFO @ Tue, 16 Jun 2020 09:42:32: 10000000 INFO @ Tue, 16 Jun 2020 09:42:37: 6000000 INFO @ Tue, 16 Jun 2020 09:42:39: 11000000 INFO @ Tue, 16 Jun 2020 09:42:40: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:42:43: 7000000 INFO @ Tue, 16 Jun 2020 09:42:45: 12000000 INFO @ Tue, 16 Jun 2020 09:42:50: 8000000 INFO @ Tue, 16 Jun 2020 09:42:50: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:42:50: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:42:50: #1 total tags in treatment: 12778785 INFO @ Tue, 16 Jun 2020 09:42:50: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:42:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:42:50: #1 tags after filtering in treatment: 12778785 INFO @ Tue, 16 Jun 2020 09:42:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:42:50: #1 finished! INFO @ Tue, 16 Jun 2020 09:42:50: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:42:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:42:51: #2 number of paired peaks: 518 WARNING @ Tue, 16 Jun 2020 09:42:51: Fewer paired peaks (518) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 518 pairs to build model! INFO @ Tue, 16 Jun 2020 09:42:51: start model_add_line... INFO @ Tue, 16 Jun 2020 09:42:51: start X-correlation... INFO @ Tue, 16 Jun 2020 09:42:51: end of X-cor INFO @ Tue, 16 Jun 2020 09:42:51: #2 finished! INFO @ Tue, 16 Jun 2020 09:42:51: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:42:51: #2 alternative fragment length(s) may be 1,17,33,548,598 bps INFO @ Tue, 16 Jun 2020 09:42:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402701/SRX5402701.10_model.r WARNING @ Tue, 16 Jun 2020 09:42:51: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:42:51: #2 You may need to consider one of the other alternative d(s): 1,17,33,548,598 WARNING @ Tue, 16 Jun 2020 09:42:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:42:51: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:42:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:42:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402701/SRX5402701.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:42:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402701/SRX5402701.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:42:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402701/SRX5402701.05_summits.bed INFO @ Tue, 16 Jun 2020 09:42:51: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:42:56: 9000000 INFO @ Tue, 16 Jun 2020 09:43:02: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:43:08: 11000000 INFO @ Tue, 16 Jun 2020 09:43:14: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:43:14: 12000000 INFO @ Tue, 16 Jun 2020 09:43:19: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:43:19: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:43:19: #1 total tags in treatment: 12778785 INFO @ Tue, 16 Jun 2020 09:43:19: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:43:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:43:19: #1 tags after filtering in treatment: 12778785 INFO @ Tue, 16 Jun 2020 09:43:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:43:19: #1 finished! INFO @ Tue, 16 Jun 2020 09:43:19: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:43:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:43:20: #2 number of paired peaks: 518 WARNING @ Tue, 16 Jun 2020 09:43:20: Fewer paired peaks (518) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 518 pairs to build model! INFO @ Tue, 16 Jun 2020 09:43:20: start model_add_line... INFO @ Tue, 16 Jun 2020 09:43:20: start X-correlation... INFO @ Tue, 16 Jun 2020 09:43:20: end of X-cor INFO @ Tue, 16 Jun 2020 09:43:20: #2 finished! INFO @ Tue, 16 Jun 2020 09:43:20: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:43:20: #2 alternative fragment length(s) may be 1,17,33,548,598 bps INFO @ Tue, 16 Jun 2020 09:43:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402701/SRX5402701.20_model.r WARNING @ Tue, 16 Jun 2020 09:43:20: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:43:20: #2 You may need to consider one of the other alternative d(s): 1,17,33,548,598 WARNING @ Tue, 16 Jun 2020 09:43:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:43:20: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:43:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:43:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402701/SRX5402701.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:43:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402701/SRX5402701.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:43:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402701/SRX5402701.10_summits.bed INFO @ Tue, 16 Jun 2020 09:43:25: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:43:43: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:43:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402701/SRX5402701.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:43:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402701/SRX5402701.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:43:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402701/SRX5402701.20_summits.bed INFO @ Tue, 16 Jun 2020 09:43:54: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling